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Background  The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq.    Results  We present a new algorithm for enumerating bubbles with length constraints in weighted directed graphs. This is the first polynomial delay algorithm for this problem and we show that in practice, it is faster than previous approaches.    Conclusion   This settles one of the main open questions from Sacomoto et al. (BMC Bioinform 13:5, 2012). Moreover, the new algorithm allows us to deal with larger instances and possibly detect longer alternative splicing events.

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs